I ended up getting a controller from Amazon.
Nintendo needs to communicate better with retailers. I don't think Amazon, Best Buy, GameStop, Target, or Wal-Mart wanted to do pre-orders because they couldn't guarantee any actual numbers on what Nintendo was sending them.
This is the same situation that's happened time and again with Amiibo, special edition 3DS consoles (Majora's Mask New 3DS comes to mind), and that GameCube controller adapter for the Wii U.
It's come down to retailers cancelling pre-orders or turning away customers which is bad business. Some retailers have given customers gift cards (Majora's Mask 3DS) in order to keep business. I don't think retailers like this. When you think about it, Nintendo's shown the least gratitude or remorse for undershipping their products. Retailers have had to take the blow because NIntendo either point fingers to the retailer or tell the customer to simply be better at refreshing their browser or being in front of a retailer two hours before they open if they want to by their products.
Nintendo's marketed the absolute hell out of this thing. They've sent review units to a number of publications. Their PR department has some vague idea of who to give them to and their reach (in subscribers).